We have an entire project devoted to MySQL 5.5 to research incorporating it into cPanel. Of note, there are considerations beyond simply adding it as an available MySQL option. For example, we need to support any prior existing variables in /etc/my.cnf that might conflict with an upgrade to MySQL 5.5 so that those systems continue to have working MySQL after such an upgrade.

We have an entire project devoted to MySQL 5.5 to research incorporating it into cPanel. Of note, there are considerations beyond simply adding it as an available MySQL option. For example, we need to support any prior existing variables in /etc/my.cnf that might conflict with an upgrade to MySQL 5.5 so that those systems continue to have working MySQL after such an upgrade.

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not sure if this would work, but why no on 5.5 upgrade, you could backup my.cnf to my.cnf-backup and then on /etc/my.cnf file do a search and replace for variable names which have changed ?